Merge branch 'develop' of https://github.com/deeptools/pyGenomeTracks …

…into updateDocBEDTools

docs/content/faq.rst

@@ -4,8 +4,8 @@ FAQ
 .. contents:: 
     :local:
 
-Why the scale of my Hi-C plot suddenly changed
-----------------------------------------------
+Why the scale of my Hi-C plot suddenly changed?
+-----------------------------------------------
 pyGenomeTracks is using `HiCMatrix <https://github.com/deeptools/HiCMatrix>`_ to read the matrix from ``h5`` and ``cool`` format.
 From version 12 to version 13, a normalization step when reading ``cool`` file was removed. This normalization was mostly used 
 when you were providing ``cool`` file from `cooler balance <https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance>`_.
@@ -22,3 +22,9 @@ If you used pyGenomeTracks version 3.5 and the last line you get is:
     INFO:pygenometracks.tracksClass:initialize x. [xxxxx]
 
 It is highly probable that BEDTools is not installed or not loaded in your environment.
+
+My Hi-C plot looks like no correction was applied when using cool matrix
+------------------------------------------------------------------------
+pyGenomeTracks is using `HiCMatrix <https://github.com/deeptools/HiCMatrix>`_ to read the matrix from ``cool`` format.
+Unfortunately, a bug was introduced in version 14 ignoring the correction factors.
+This bug was fixed in version 15 so update HiCMatrix to last version should fix it.

pygenometracks/getAllDefaultsAndPossible.py

@@ -85,7 +85,7 @@ def main():
 
     # For the default they are summarized in a matrix
     mat = np.empty((len(all_default_parameters) + 2, len(all_tracks_with_default) + 1),
-                   dtype='U25')
+                   dtype='U100')
     mat[0, 0] = 'parameter'
     mat[1, 0] = '--'
     for j, track_type in enumerate(all_tracks_with_default, start=1):

pygenometracks/tracks/BedGraphTrack.py

@@ -140,15 +140,13 @@ def __init__(self, properties_dict):
                                  " requires to set the parameter"
                                  " second_file.")
             else:
-                if self.properties['second_file'].endswith(".bgz"):
+                # First try to open it as a Tabix file
+                try:
                     # from the tabix file is not possible to know the
                     # global min and max
-                    try:
-                        self.tbx2 = pysam.TabixFile(self.properties['second_file'])
-                    except IOError:
-                        self.interval_tree2, __, __ = file_to_intervaltree(self.properties['second_file'])
-                # load the file as an interval tree
-                else:
+                    self.tbx2 = pysam.TabixFile(self.properties['second_file'])
+                except IOError:
+                    # load the file as an interval tree
                     self.interval_tree2, __, __ = file_to_intervaltree(self.properties['second_file'])
 
     def set_properties_defaults(self):
@@ -183,17 +181,13 @@ def set_properties_defaults(self):
 
     def load_file(self):
         self.tbx = None
-        # try to load a tabix file is available
-        if self.properties['file'].endswith(".bgz"):
+        # try to load a tabix file if available
+        try:
             # from the tabix file is not possible to know the
             # global min and max
-            try:
-                self.tbx = pysam.TabixFile(self.properties['file'])
-            except IOError:
-                self.interval_tree, __, __ = file_to_intervaltree(self.properties['file'],
-                                                                  self.properties['region'])
-        # load the file as an interval tree
-        else:
+            self.tbx = pysam.TabixFile(self.properties['file'])
+        except IOError:
+            # load the file as an interval tree
             self.interval_tree, __, __ = file_to_intervaltree(self.properties['file'],
                                                               self.properties['region'])
 

pygenometracks/utilities.py

@@ -7,6 +7,13 @@
 import pybedtools
 import tempfile
 import warnings
+import logging
+
+
+FORMAT = "[%(levelname)s:%(filename)s:%(lineno)s - %(funcName)20s()] %(message)s"
+logging.basicConfig(format=FORMAT)
+log = logging.getLogger(__name__)
+log.setLevel(logging.DEBUG)
 
 
 class InputError(Exception):
@@ -86,6 +93,13 @@ def temp_file_from_intersect(file_name, plot_regions=None, around_region=0):
             file_to_open = original_file.intersect(regions, wa=True, u=True).fn
         except pybedtools.helpers.BEDToolsError:
             file_to_open = file_name
+        except NotImplementedError as e:
+            log.error("BEDTools is not installed but required.")
+            raise e
+        except Exception as e:
+            log.warning(f"BEDTools intersect raised: {e}"
+                        "\nWill not subset the file.")
+            file_to_open = file_name
         sys.stderr.close()
         sys.stderr = sys.__stderr__
         with open(temporary_file.name, 'r') as f:
@@ -94,9 +108,9 @@ def temp_file_from_intersect(file_name, plot_regions=None, around_region=0):
         error_lines = [line for line in temp_std_error if 'error' in line.lower()]
         if len(error_lines) > 0:
             error_lines_printable = '\n'.join(error_lines)
-            sys.stderr.write("Bedtools intersect raised an error:\n"
-                             f"{error_lines_printable}\n"
-                             "Will not use bedtools.\n")
+            log.warning("BEDTools intersect raised an error:\n"
+                        f"{error_lines_printable}\n"
+                        "Will not use BEDTools.\n")
             file_to_open = file_name
     return file_to_open
 
@@ -171,7 +185,11 @@ def file_to_intervaltree(file_name, plot_regions=None):
         valid_intervals += 1
 
     if valid_intervals == 0:
-        sys.stderr.write(f"No valid intervals were found in file {file_name}")
+        if file_to_open == file_name:
+            suffix = " after intersection with the plotted region"
+        else:
+            suffix = ""
+        log.warning(f"No valid intervals were found in file {file_name}{suffix}")
     file_h.close()
 
     return interval_tree, min_value, max_value

requirements.txt

@@ -8,4 +8,4 @@ pysam >=0.14
 gffutils >=0.9
 pybedtools >=0.8.1
 tqdm >=4.20
-libopenblas < 0.3.10
+